Wheels are not being built properly

[wasade]

This has been holding up a 2.1.16 release. No time to do it right now, and this would represent at least 1.5 week delay. Deferring a fix to later.

[pkirti33]

I am having this issue when using "pip install biom-format" into my virtual environment. I am getting several error messages, which include:

Building wheel for biom-format (pyproject.toml) did not run successfully. Python recognizes 'biom.assets' as an importable package[^1], but it is absent from setuptools' packages configuration. Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools' packages configuration. Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools' packages configuration.

[wasade]

Thanks, good catch. What operating system, and version of python?On Jun 7, 2024, at 10:00, pkirti33 @.***> wrote: I am having this issue when using "pip install biom-format" into my virtual environment. I am getting several error messages, which include: Building wheel for biom-format (pyproject.toml) did not run successfully. Python recognizes 'biom.assets' as an importable package[^1], but it is absent from setuptools' packages configuration. Python recognizes 'biom.tests.bench_tables' as an importable package[^1], but it is absent from setuptools' packages configuration. Python recognizes 'biom.tests.test_cli.test_data' as an importable package[^1], but it is absent from setuptools' packages configuration.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: @.***>

[pkirti33]

Sorry for not including that!

• Operating system: Windows 10 Enterprise
• Python version: 3.11.9

[wasade]

Thanks. Is this within WSL?

[pkirti33]

No - I'm running my commands directly in Windows Command Prompt

[wasade]

We test against windows-latest which is Windows 2022. However, we don't have any Windows systems locally.

We are not instrumented to assert wheels build correctly, and as noted in this issue, we did not push wheels for this latest release. Could you attempt installing natively as done in the CI action and see if that works (e.g., git clone https://github.com/biocore/biom-format.git; cd biom-format; pip install .)? Alternatively, can you install from conda?

[pkirti33]

Hi, Thanks for your prompt replies! Installing it natively didn't work - I ran into the same issues. One thing that might be noteworthy is that my project uses a pyproject.toml file. The last line of my error message states:

ERROR: Could not build wheels for biom-format, which is required to install pyproject.toml-based projects

[wasade]

Any chance you'd be interested in futzing with setup.py and pyproject.toml in your local clone to see if you can find something which works, and issue a pull request?

[pkirti33]

Hello, Thank you for your help, I think I found a workaround. biom-format is pre-installed in qiime2 (which I'm using), so I'm just going to perform my operations within that venv. Thank you!

[wasade]

Sounds good, thanks!

[schlich]

This still seems to be an issue and is causing failures installing scikit-bio, I'm getting very similar error messages + missing gcc

[wasade]

Could you open an issue with scikit-bio?

[schlich]

I don't think it's an issue with scikit-bio. Do they maintain this repository?

[schlich]

There is a stack trace in the linked issue above, i'm not sure why it would be appropriate to bring this up over there unless i'm really misunderstanding the problem. Plus, there is already this issue here.

[wasade]

You said you were having an issue installing scikit-bio?

I would welcome a PR to restore wheel builds, but I am currently on leave and cannot do it myself anytime soon

[schlich]

Sorry for the confusion, scikit-bio was failing to install because it depends on biom-format which is failing to build. Happy to take a stab at a PR for you!

[wasade]

Thanks! The scikit-bio team would value feedback though if their installation instructions are not covering your environment

[schlich]

@wasade that wasn't too bad, builds all seemed to work locally, tried to keep configurations as close to the same as i could just focusing on moving to pyproject.toml and getting cibuildtool in there.

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